Starting phenix.real_space_refine on Fri Dec 27 08:09:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qw4_18680/12_2024/8qw4_18680.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qw4_18680/12_2024/8qw4_18680.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qw4_18680/12_2024/8qw4_18680.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qw4_18680/12_2024/8qw4_18680.map" model { file = "/net/cci-nas-00/data/ceres_data/8qw4_18680/12_2024/8qw4_18680.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qw4_18680/12_2024/8qw4_18680.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 27 5.16 5 C 2286 2.51 5 N 564 2.21 5 O 602 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3479 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2591 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 13, 'TRANS': 306} Chain breaks: 4 Chain: "B" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 888 Classifications: {'peptide': 114} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 111} Chain breaks: 1 Time building chain proxies: 5.13, per 1000 atoms: 1.47 Number of scatterers: 3479 At special positions: 0 Unit cell: (93.072, 57.339, 101.382, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 27 16.00 O 602 8.00 N 564 7.00 C 2286 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 165 " - pdb=" SG CYS A 185 " distance=2.03 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 264 " distance=2.04 Simple disulfide: pdb=" SG CYS A 286 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 98 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 420.6 milliseconds 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 808 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 4 sheets defined 52.5% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 195 through 225 removed outlier: 3.885A pdb=" N LEU A 199 " --> pdb=" O ARG A 195 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR A 204 " --> pdb=" O SER A 200 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N GLY A 207 " --> pdb=" O ARG A 203 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ILE A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR A 220 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE A 221 " --> pdb=" O THR A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 253 removed outlier: 3.963A pdb=" N PHE A 240 " --> pdb=" O ARG A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 256 No H-bonds generated for 'chain 'A' and resid 254 through 256' Processing helix chain 'A' and resid 283 through 313 removed outlier: 3.615A pdb=" N THR A 287 " --> pdb=" O ASN A 283 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET A 288 " --> pdb=" O LYS A 284 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU A 289 " --> pdb=" O ALA A 285 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE A 290 " --> pdb=" O CYS A 286 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N MET A 291 " --> pdb=" O THR A 287 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ILE A 292 " --> pdb=" O MET A 288 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N PHE A 295 " --> pdb=" O MET A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 326 Processing helix chain 'A' and resid 327 through 345 Proline residue: A 339 - end of helix Processing helix chain 'A' and resid 367 through 375 removed outlier: 3.625A pdb=" N LEU A 371 " --> pdb=" O ASP A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 402 removed outlier: 4.147A pdb=" N SER A 396 " --> pdb=" O ALA A 392 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG A 399 " --> pdb=" O ILE A 395 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N VAL A 400 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ILE A 402 " --> pdb=" O ASN A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 411 Processing helix chain 'A' and resid 413 through 443 removed outlier: 4.077A pdb=" N PHE A 417 " --> pdb=" O LYS A 413 " (cutoff:3.500A) Proline residue: A 431 - end of helix Processing helix chain 'A' and resid 445 through 452 removed outlier: 3.647A pdb=" N TRP A 449 " --> pdb=" O TYR A 445 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU A 450 " --> pdb=" O ARG A 446 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR A 451 " --> pdb=" O GLY A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 457 Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.533A pdb=" N LEU A 479 " --> pdb=" O PRO A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 489 removed outlier: 3.598A pdb=" N TYR A 484 " --> pdb=" O PHE A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 493 Proline residue: A 493 - end of helix No H-bonds generated for 'chain 'A' and resid 490 through 493' Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'B' and resid 89 through 93 Processing sheet with id=AA1, first strand: chain 'A' and resid 177 through 178 removed outlier: 6.357A pdb=" N TYR A 177 " --> pdb=" O CYS A 185 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 22 through 27 removed outlier: 4.382A pdb=" N ASP B 79 " --> pdb=" O ALA B 27 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 61 through 62 removed outlier: 6.821A pdb=" N TRP B 39 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ASP B 53 " --> pdb=" O MET B 37 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N MET B 37 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL B 36 " --> pdb=" O GLU B 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 94 through 95 156 hydrogen bonds defined for protein. 438 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.91 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 1034 1.34 - 1.46: 921 1.46 - 1.59: 1564 1.59 - 1.71: 0 1.71 - 1.83: 41 Bond restraints: 3560 Sorted by residual: bond pdb=" N GLU A 407 " pdb=" CA GLU A 407 " ideal model delta sigma weight residual 1.460 1.486 -0.026 1.50e-02 4.44e+03 2.99e+00 bond pdb=" C ASP A 476 " pdb=" N LEU A 477 " ideal model delta sigma weight residual 1.331 1.307 0.024 1.40e-02 5.10e+03 2.97e+00 bond pdb=" C LEU A 406 " pdb=" N GLU A 407 " ideal model delta sigma weight residual 1.330 1.351 -0.021 1.28e-02 6.10e+03 2.77e+00 bond pdb=" CB THR A 276 " pdb=" CG2 THR A 276 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.63e+00 bond pdb=" CB TYR A 177 " pdb=" CG TYR A 177 " ideal model delta sigma weight residual 1.512 1.477 0.035 2.20e-02 2.07e+03 2.48e+00 ... (remaining 3555 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 4614 2.38 - 4.76: 169 4.76 - 7.14: 31 7.14 - 9.52: 5 9.52 - 11.91: 3 Bond angle restraints: 4822 Sorted by residual: angle pdb=" C GLU A 235 " pdb=" N ARG A 236 " pdb=" CA ARG A 236 " ideal model delta sigma weight residual 120.09 125.89 -5.80 1.25e+00 6.40e-01 2.15e+01 angle pdb=" N ARG A 459 " pdb=" CA ARG A 459 " pdb=" C ARG A 459 " ideal model delta sigma weight residual 110.80 101.02 9.78 2.13e+00 2.20e-01 2.11e+01 angle pdb=" N GLY A 354 " pdb=" CA GLY A 354 " pdb=" C GLY A 354 " ideal model delta sigma weight residual 112.13 118.02 -5.89 1.34e+00 5.57e-01 1.93e+01 angle pdb=" C ALA B 43 " pdb=" N PRO B 44 " pdb=" CA PRO B 44 " ideal model delta sigma weight residual 127.00 136.73 -9.73 2.40e+00 1.74e-01 1.64e+01 angle pdb=" C CYS A 458 " pdb=" N ARG A 459 " pdb=" CA ARG A 459 " ideal model delta sigma weight residual 121.54 129.22 -7.68 1.91e+00 2.74e-01 1.62e+01 ... (remaining 4817 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.29: 1877 16.29 - 32.57: 177 32.57 - 48.86: 30 48.86 - 65.14: 4 65.14 - 81.43: 6 Dihedral angle restraints: 2094 sinusoidal: 837 harmonic: 1257 Sorted by residual: dihedral pdb=" CB CYS A 189 " pdb=" SG CYS A 189 " pdb=" SG CYS A 264 " pdb=" CB CYS A 264 " ideal model delta sinusoidal sigma weight residual -86.00 -157.10 71.10 1 1.00e+01 1.00e-02 6.49e+01 dihedral pdb=" CA TYR A 177 " pdb=" C TYR A 177 " pdb=" N SER A 178 " pdb=" CA SER A 178 " ideal model delta harmonic sigma weight residual -180.00 -145.73 -34.27 0 5.00e+00 4.00e-02 4.70e+01 dihedral pdb=" CA SER A 178 " pdb=" C SER A 178 " pdb=" N PHE A 179 " pdb=" CA PHE A 179 " ideal model delta harmonic sigma weight residual -180.00 -146.92 -33.08 0 5.00e+00 4.00e-02 4.38e+01 ... (remaining 2091 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 361 0.048 - 0.096: 136 0.096 - 0.144: 34 0.144 - 0.192: 17 0.192 - 0.241: 2 Chirality restraints: 550 Sorted by residual: chirality pdb=" CA VAL A 316 " pdb=" N VAL A 316 " pdb=" C VAL A 316 " pdb=" CB VAL A 316 " both_signs ideal model delta sigma weight residual False 2.44 2.20 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" CA PRO B 90 " pdb=" N PRO B 90 " pdb=" C PRO B 90 " pdb=" CB PRO B 90 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA PRO A 405 " pdb=" N PRO A 405 " pdb=" C PRO A 405 " pdb=" CB PRO A 405 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 9.11e-01 ... (remaining 547 not shown) Planarity restraints: 587 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 316 " -0.077 5.00e-02 4.00e+02 1.16e-01 2.14e+01 pdb=" N PRO A 317 " 0.200 5.00e-02 4.00e+02 pdb=" CA PRO A 317 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO A 317 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 474 " 0.035 5.00e-02 4.00e+02 5.29e-02 4.47e+00 pdb=" N PRO A 475 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 475 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 475 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 428 " 0.010 2.00e-02 2.50e+03 1.41e-02 3.99e+00 pdb=" CG TYR A 428 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR A 428 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR A 428 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR A 428 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 428 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR A 428 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 428 " -0.001 2.00e-02 2.50e+03 ... (remaining 584 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 75 2.65 - 3.21: 3457 3.21 - 3.78: 5258 3.78 - 4.34: 7053 4.34 - 4.90: 11275 Nonbonded interactions: 27118 Sorted by model distance: nonbonded pdb=" O GLN A 455 " pdb=" NH2 ARG A 459 " model vdw 2.091 3.120 nonbonded pdb=" OH TYR A 241 " pdb=" O VAL A 490 " model vdw 2.209 3.040 nonbonded pdb=" O ASN A 410 " pdb=" N LYS A 413 " model vdw 2.275 3.120 nonbonded pdb=" O ASP A 260 " pdb=" NH1 ARG A 261 " model vdw 2.288 3.120 nonbonded pdb=" O THR A 217 " pdb=" OG1 THR A 220 " model vdw 2.300 3.040 ... (remaining 27113 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 15.250 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6284 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 3560 Z= 0.479 Angle : 1.098 11.906 4822 Z= 0.608 Chirality : 0.058 0.241 550 Planarity : 0.008 0.116 587 Dihedral : 13.197 81.429 1274 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.05 % Favored : 85.95 % Rotamer: Outliers : 0.26 % Allowed : 0.00 % Favored : 99.74 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.49 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.39), residues: 420 helix: -0.99 (0.37), residues: 189 sheet: -1.69 (0.86), residues: 38 loop : -3.62 (0.39), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 104 HIS 0.003 0.001 HIS A 282 PHE 0.020 0.003 PHE A 201 TYR 0.034 0.003 TYR A 428 ARG 0.009 0.001 ARG B 41 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 ARG cc_start: 0.6980 (tpt90) cc_final: 0.5436 (mtp180) REVERT: A 336 TRP cc_start: 0.7890 (m100) cc_final: 0.7653 (m-10) REVERT: A 349 MET cc_start: 0.4417 (mmt) cc_final: 0.3595 (ptt) REVERT: A 442 GLU cc_start: 0.7268 (mt-10) cc_final: 0.6685 (mp0) REVERT: B 35 ASP cc_start: 0.7720 (m-30) cc_final: 0.7504 (m-30) REVERT: B 55 THR cc_start: 0.7761 (p) cc_final: 0.7495 (m) outliers start: 1 outliers final: 2 residues processed: 119 average time/residue: 0.9265 time to fit residues: 114.1683 Evaluate side-chains 66 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain A residue 352 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 0.2980 chunk 18 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 0.3980 chunk 20 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN ** A 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6306 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 3560 Z= 0.287 Angle : 0.879 8.375 4822 Z= 0.448 Chirality : 0.051 0.189 550 Planarity : 0.007 0.069 587 Dihedral : 7.421 36.115 478 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 5.01 % Allowed : 17.94 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.39), residues: 420 helix: -0.77 (0.37), residues: 191 sheet: -1.06 (0.85), residues: 38 loop : -3.34 (0.40), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 449 HIS 0.001 0.001 HIS A 282 PHE 0.026 0.002 PHE B 32 TYR 0.018 0.002 TYR A 428 ARG 0.006 0.001 ARG B 48 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 0.393 Fit side-chains REVERT: A 203 ARG cc_start: 0.7066 (tpt90) cc_final: 0.5550 (mtp180) REVERT: A 349 MET cc_start: 0.4575 (mmt) cc_final: 0.3554 (ptt) REVERT: A 415 VAL cc_start: 0.5530 (OUTLIER) cc_final: 0.4315 (t) outliers start: 19 outliers final: 7 residues processed: 81 average time/residue: 1.0192 time to fit residues: 85.6146 Evaluate side-chains 73 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 102 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 21 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 26 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 39 optimal weight: 0.3980 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN A 332 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6353 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3560 Z= 0.278 Angle : 0.834 8.214 4822 Z= 0.424 Chirality : 0.050 0.294 550 Planarity : 0.006 0.061 587 Dihedral : 7.056 33.347 476 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % Rotamer: Outliers : 4.75 % Allowed : 22.43 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.40), residues: 420 helix: -0.45 (0.38), residues: 190 sheet: -1.10 (0.82), residues: 36 loop : -3.28 (0.41), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 449 HIS 0.002 0.001 HIS A 282 PHE 0.021 0.002 PHE B 32 TYR 0.022 0.002 TYR A 428 ARG 0.005 0.001 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 ARG cc_start: 0.7003 (tpt90) cc_final: 0.5578 (tpt-90) REVERT: A 349 MET cc_start: 0.4318 (mmt) cc_final: 0.3822 (ptt) REVERT: A 415 VAL cc_start: 0.5393 (OUTLIER) cc_final: 0.4124 (t) REVERT: A 433 LEU cc_start: 0.7702 (tm) cc_final: 0.7493 (pp) outliers start: 18 outliers final: 5 residues processed: 83 average time/residue: 0.9053 time to fit residues: 78.2334 Evaluate side-chains 68 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 102 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 38 optimal weight: 0.0010 chunk 29 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 0.4980 chunk 39 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6346 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3560 Z= 0.257 Angle : 0.823 9.923 4822 Z= 0.410 Chirality : 0.047 0.173 550 Planarity : 0.005 0.058 587 Dihedral : 6.647 26.093 473 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 5.80 % Allowed : 24.01 % Favored : 70.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.41), residues: 420 helix: -0.26 (0.38), residues: 189 sheet: -0.88 (0.85), residues: 36 loop : -3.06 (0.42), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 449 HIS 0.001 0.000 HIS A 282 PHE 0.015 0.002 PHE B 32 TYR 0.012 0.002 TYR A 245 ARG 0.005 0.000 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 70 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: A 203 ARG cc_start: 0.7080 (OUTLIER) cc_final: 0.5541 (tpt-90) REVERT: A 349 MET cc_start: 0.4364 (mmt) cc_final: 0.3442 (ptt) REVERT: A 415 VAL cc_start: 0.5470 (OUTLIER) cc_final: 0.4146 (t) REVERT: A 428 TYR cc_start: 0.7724 (t80) cc_final: 0.7475 (t80) REVERT: A 433 LEU cc_start: 0.7871 (tm) cc_final: 0.7617 (pp) outliers start: 22 outliers final: 8 residues processed: 81 average time/residue: 0.9385 time to fit residues: 78.9157 Evaluate side-chains 70 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 102 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 23 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 17 optimal weight: 0.2980 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 0.0000 chunk 21 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6349 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3560 Z= 0.249 Angle : 0.820 9.700 4822 Z= 0.407 Chirality : 0.047 0.173 550 Planarity : 0.005 0.058 587 Dihedral : 6.468 27.964 473 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 6.07 % Allowed : 27.97 % Favored : 65.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.41), residues: 420 helix: -0.19 (0.39), residues: 189 sheet: -0.69 (0.87), residues: 36 loop : -3.00 (0.44), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 449 HIS 0.001 0.000 HIS A 282 PHE 0.025 0.002 PHE A 224 TYR 0.013 0.002 TYR A 241 ARG 0.005 0.000 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 63 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 203 ARG cc_start: 0.7122 (OUTLIER) cc_final: 0.5601 (tpt-90) REVERT: A 349 MET cc_start: 0.4424 (mmt) cc_final: 0.3469 (ptt) REVERT: A 415 VAL cc_start: 0.5545 (OUTLIER) cc_final: 0.4218 (t) REVERT: A 428 TYR cc_start: 0.7707 (t80) cc_final: 0.7462 (t80) REVERT: A 433 LEU cc_start: 0.7819 (tm) cc_final: 0.7576 (pp) outliers start: 23 outliers final: 11 residues processed: 76 average time/residue: 0.8740 time to fit residues: 69.2494 Evaluate side-chains 73 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 108 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 0.9990 chunk 10 optimal weight: 0.0570 chunk 41 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 23 optimal weight: 0.0870 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6366 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3560 Z= 0.254 Angle : 0.823 9.934 4822 Z= 0.406 Chirality : 0.047 0.172 550 Planarity : 0.005 0.060 587 Dihedral : 6.397 28.279 473 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 5.54 % Allowed : 27.97 % Favored : 66.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.42), residues: 420 helix: -0.12 (0.39), residues: 189 sheet: -0.70 (0.87), residues: 36 loop : -2.96 (0.45), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 453 HIS 0.001 0.000 HIS A 282 PHE 0.014 0.002 PHE A 221 TYR 0.013 0.001 TYR A 245 ARG 0.006 0.000 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 ARG cc_start: 0.7162 (OUTLIER) cc_final: 0.5611 (tpt-90) REVERT: A 349 MET cc_start: 0.4379 (mmt) cc_final: 0.3479 (ptt) REVERT: A 415 VAL cc_start: 0.5623 (OUTLIER) cc_final: 0.4240 (t) REVERT: A 428 TYR cc_start: 0.7723 (t80) cc_final: 0.7492 (t80) REVERT: A 433 LEU cc_start: 0.7774 (tm) cc_final: 0.7546 (pp) outliers start: 21 outliers final: 12 residues processed: 80 average time/residue: 0.8701 time to fit residues: 72.4889 Evaluate side-chains 73 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 108 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 30 optimal weight: 0.6980 chunk 23 optimal weight: 0.2980 chunk 35 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 25 optimal weight: 0.1980 chunk 19 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 8 optimal weight: 0.0370 chunk 26 optimal weight: 0.5980 overall best weight: 0.3458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6331 moved from start: 0.4726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3560 Z= 0.239 Angle : 0.862 10.632 4822 Z= 0.419 Chirality : 0.047 0.173 550 Planarity : 0.005 0.058 587 Dihedral : 6.282 28.324 473 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 6.07 % Allowed : 27.18 % Favored : 66.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.42), residues: 420 helix: -0.13 (0.39), residues: 189 sheet: -0.50 (0.86), residues: 35 loop : -3.01 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 304 HIS 0.001 0.000 HIS A 282 PHE 0.015 0.002 PHE A 224 TYR 0.013 0.001 TYR A 445 ARG 0.007 0.000 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 65 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 ARG cc_start: 0.7089 (OUTLIER) cc_final: 0.5539 (tpt-90) REVERT: A 349 MET cc_start: 0.4362 (mmt) cc_final: 0.3479 (ptt) REVERT: A 428 TYR cc_start: 0.7712 (t80) cc_final: 0.7481 (t80) REVERT: A 433 LEU cc_start: 0.7764 (tm) cc_final: 0.7560 (pp) outliers start: 23 outliers final: 11 residues processed: 81 average time/residue: 0.9221 time to fit residues: 77.6708 Evaluate side-chains 70 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 CYS Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 108 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 28 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 32 optimal weight: 0.0470 chunk 37 optimal weight: 0.2980 chunk 39 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 23 optimal weight: 0.0070 chunk 16 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 overall best weight: 0.3096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6309 moved from start: 0.4989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3560 Z= 0.235 Angle : 0.855 11.560 4822 Z= 0.412 Chirality : 0.045 0.174 550 Planarity : 0.005 0.060 587 Dihedral : 6.062 27.807 473 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 4.22 % Allowed : 30.87 % Favored : 64.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.42), residues: 420 helix: -0.09 (0.39), residues: 189 sheet: -0.45 (0.87), residues: 35 loop : -2.98 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 304 HIS 0.001 0.000 HIS A 332 PHE 0.018 0.002 PHE A 240 TYR 0.013 0.001 TYR A 245 ARG 0.005 0.000 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: A 203 ARG cc_start: 0.7101 (OUTLIER) cc_final: 0.5540 (tpt-90) REVERT: A 224 PHE cc_start: 0.7761 (OUTLIER) cc_final: 0.7389 (t80) REVERT: A 349 MET cc_start: 0.4341 (mmt) cc_final: 0.3501 (ptt) REVERT: A 433 LEU cc_start: 0.7754 (tm) cc_final: 0.7551 (pp) outliers start: 16 outliers final: 9 residues processed: 82 average time/residue: 0.9213 time to fit residues: 78.5356 Evaluate side-chains 74 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 CYS Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 224 PHE Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 108 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 11 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6406 moved from start: 0.5051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 3560 Z= 0.310 Angle : 0.984 11.265 4822 Z= 0.472 Chirality : 0.049 0.166 550 Planarity : 0.006 0.062 587 Dihedral : 6.460 28.164 473 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.48 % Favored : 89.52 % Rotamer: Outliers : 4.49 % Allowed : 31.93 % Favored : 63.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.42), residues: 420 helix: -0.15 (0.39), residues: 189 sheet: -0.63 (0.86), residues: 35 loop : -3.09 (0.43), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 104 HIS 0.002 0.001 HIS A 282 PHE 0.009 0.002 PHE A 480 TYR 0.032 0.002 TYR A 428 ARG 0.006 0.000 ARG A 183 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 203 ARG cc_start: 0.7116 (OUTLIER) cc_final: 0.5554 (tpt-90) REVERT: A 349 MET cc_start: 0.4427 (mmt) cc_final: 0.3599 (ptt) REVERT: A 433 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7572 (pp) outliers start: 17 outliers final: 9 residues processed: 82 average time/residue: 0.8801 time to fit residues: 75.0277 Evaluate side-chains 70 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 CYS Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 108 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 34 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 36 optimal weight: 0.4980 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 5 optimal weight: 0.0870 chunk 9 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6397 moved from start: 0.5337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 3560 Z= 0.285 Angle : 0.990 13.778 4822 Z= 0.472 Chirality : 0.050 0.182 550 Planarity : 0.005 0.061 587 Dihedral : 6.368 27.186 473 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 3.96 % Allowed : 33.51 % Favored : 62.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.41), residues: 420 helix: -0.19 (0.39), residues: 189 sheet: -0.63 (0.86), residues: 35 loop : -3.05 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 453 HIS 0.001 0.000 HIS A 282 PHE 0.010 0.002 PHE A 194 TYR 0.035 0.002 TYR A 428 ARG 0.008 0.001 ARG A 183 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: A 203 ARG cc_start: 0.7108 (OUTLIER) cc_final: 0.5486 (tpt-90) REVERT: A 291 MET cc_start: 0.6151 (OUTLIER) cc_final: 0.5760 (pmm) REVERT: A 349 MET cc_start: 0.4355 (mmt) cc_final: 0.3537 (ptt) REVERT: A 433 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7593 (pp) outliers start: 15 outliers final: 8 residues processed: 73 average time/residue: 0.9020 time to fit residues: 68.5630 Evaluate side-chains 70 residues out of total 379 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 CYS Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 291 MET Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 108 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 35 optimal weight: 1.9990 chunk 4 optimal weight: 0.0170 chunk 6 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 22 optimal weight: 0.0270 chunk 27 optimal weight: 0.4980 chunk 26 optimal weight: 0.6980 chunk 16 optimal weight: 0.0980 overall best weight: 0.2676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.183322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.168575 restraints weight = 8015.143| |-----------------------------------------------------------------------------| r_work (start): 0.4345 rms_B_bonded: 3.55 r_work: 0.4251 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.4251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 moved from start: 0.5516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3560 Z= 0.249 Angle : 0.968 11.961 4822 Z= 0.457 Chirality : 0.048 0.178 550 Planarity : 0.005 0.055 587 Dihedral : 6.049 26.512 473 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 3.69 % Allowed : 34.30 % Favored : 62.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.42), residues: 420 helix: -0.15 (0.39), residues: 189 sheet: -0.70 (0.84), residues: 35 loop : -3.02 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 311 HIS 0.001 0.000 HIS A 332 PHE 0.016 0.002 PHE A 296 TYR 0.020 0.002 TYR A 428 ARG 0.008 0.001 ARG A 183 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2195.16 seconds wall clock time: 39 minutes 55.78 seconds (2395.78 seconds total)